Table 2.
Sequence statistics
| FF‐CT | FF‐NT | FFPE‐CT | FFPE‐NT | |
|---|---|---|---|---|
| Median insert size | 145.3 ± 1.1 | 147.8 ± 3.3 | 127.3 ± 2.9 | 128.5 ± 2.7 |
| Total raw reads | 60,701,176 ± 2,611,637 | 61,386,410 ± 3,225,703 | 56,042,463 ± 3,217,046 | 52,955,491 ± 2,097,483 |
| Mapped reads | 57,663,943 ± 2,875,484 | 58,101,677 ± 2,583,479 | 47,686,960 ± 3,607,514 | 45,190,024 ± 1,783,127 |
| % of mapped reads | 95.0 ± 0.9 | 94.7 ± 0.8 | 85.0 ± 2.4 | 85.3 ± 1.1 |
| Remaining reads after clipping | 52,155,448 ± 3,444,210 | 45,920,354 ± 5,464,927 | 13,590,626 ± 1,911,843 | 13,689,569 ± 3,818,050 |
| % of duplicated reads | 9.6 ± 2.1 | 21.0 ± 8.4 | 64.5 ± 4.4 | 61.5 ± 2.6 |
| Genome size | 3,137,503,007 | 3,137,503,007 | 3,137,503,007 | 3,137,503,007 |
| Mapped bases passed through a filter | 3,974,470,410 ± 287,091,192 | 3,553,923,182 ± 414,817,717 | 894,631,300 ± 146,916,493 | 918,060,184 ± 277,587,019 |
| On‐target bases (%) | 3,178,559,259 ± 214,364,542 (80.0 ± 0.5) | 2,824,621,506 ± 337,411,613 (79.5 ± 0.7) | 608,073,556 ± 100,282,511 (68.0 ± 0.9) | 619,774,900 ± 202,754,019 (67.1 ± 1.6) |
| Near‐target bases# (%) | 547,441,692 ± 47,772,892 (13.8 ± 0.5) | 495,694,119 ± 62,502,784 (13.9 ± 0.5) | 87,521,342 ± 16,770,315 (9.8 ± 0.4) | 91,630,733 ± 30,598,132 (9.9 ± 0.3) |
| Off‐target bases (%) | 248,469,459 ± 27,983,602 (6.2 ± 0.3) | 233,607,557 ± 20,337,832 (6.6 ± 0.3) | 199,036,402 ± 31,488,025 (22.3 ± 0.9) | 248,469,459 ± 27,983,605 (23.0 ± 1.9) |
| Mean on‐target coverage | 37.6 ± 2.6 | 33.5 ± 4.0 | 7.2 ± 1.2 | 7.3 ± 2.4 |
| Number of CpG sites on Methyl‐Seq probe | ~ 3.7 Million | ~ 3.7 Million | ~ 3.7 Million | ~ 3.7 Million |
| Number of CpG sites (1× depth) | 3,682,842 ± 38,116 | 3,622,934 ± 51,977 | 3,040,326 ± 130,104 | 2,937,087 ± 127,111 |
| Number of CpG sites (>6× depth) | 2,884,711 ± 18,924 | 2,876,447 ± 26,253 | 1,611,751 ± 254,405 | 1,517,406 ± 356,333 |
#
Near‐target bases are defined as the detected bases mapped within 1 kb upstream or downstream of Agilent ready‐made probes. FF‐CT, fresh‐frozen cancer tissue; FF‐NT, fresh‐frozen non‐cancerous tissue; FFPE‐CT, formalin‐fixed paraffin‐embedded cancer tissue; FFPE‐NT, formalin‐fixed paraffin‐embedded non‐cancerous tissue.